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| - | {{ETHZ_Basel10}}
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| - | {{ETHZ_Basel10_Empty}}
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| - | = Internal =
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| - | This section will be removed before wiki-freeze!
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| - |
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| - | = Acknowledged problems/incomplete pages =
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Movement#Direction_changes plot (weird for tumbling state)
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| - | ** Responsible: Simona
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| - | <br>
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| - |
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| - | = General remarks =
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| - | * '''Protein names''': normally written
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| - | * '''gene names''': italic
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| - | * '''Directed movement''' NOT running, please correct!
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| - | * '''chemotaxis''' pathway NOT Chemotaxis nor chemotactic
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| - | * '''E. lemming''' with space
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| - | * E. lemming vs THE E. lemming: E. lemming: Project name (whole assay), The E. lemming: One single genetically modified ''E. coli''
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| - | * '''far-red light''', not far red light, please correct!
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| - | * '''internal links''' - we should refer to other internal pages (hyperlinks) where appropriate, inside the paragraphs.
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| - |
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| - | = Suggestions =
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| - |
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| - | * We need to be consistent in the use of formal/informal language. what do you decide upon this?
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology: '''Elsa'''
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| - | first paragraph, define 'anchor' and 'tumbling' and 'directed movement' before using the terms
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| - | <br>second paragraph: quite unclear, if possible, add more details & explain more
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| - | <br>add a few sentences (and link them) regarding ARL & Safety
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing
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| - | 50 μm (?) high flow channel; remove question mark
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/InformationFlow
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| - | in second part of the page, 'cells with highest score'; define the score
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| - | <br>clearly define the reference used: [1] Stuurman et al. 2007; could not uniquely identify it
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Light_Switch
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| - | Original sentence 'It should be noticed that this signal changes with time constant in the range of hours' rephrased to:'It should be noticed that this signal constantly changes with time in the range of hours.' Revert if meaning changed.
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology/Implementation
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| - | added reference [2]. would be good if a biologist can check if it's the right one. Looks like the page ends abruptly. something like a conclusion perhaps?
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Visualization
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| - | spacing, subheadings & some bullet points); suggesting more images for the user experience part
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/CellDetection
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| - | Corrected minor spelling mistakes. Gave names to the 2 steps of the cell detection algorithm. Added subheadings to make it more readable & structured. Revert if necessary.
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Achievements/Medal_Criteria
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| - | check with biology to keep it updated (check list)
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Team
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| - | Add link to Biozentrum Unibas.
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| - |
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| - | = Teaser & Motivation =
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| - |
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| - | ==Images==
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| - | '''Simona''': Achievements image: increase resolution; Same for first image. (Response from George: resolution was decreased to match to LowRes Lemmings screenshot. It looks incoherent, if only E. lemming is HighRes. See [https://static.igem.org/mediawiki/2010/archive/8/84/20101022190334!ETHZ_Basel_teaser_project.png this version.])
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| - |
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| - | '''Thanuja''': a better picture to suggest what we have done? any creative ideas to make a better first impression? (Response from George: Yes, please make suggestions! I ran out of ideas. ;-))
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| - | '''Simona''': pictures look very cool; if possible, change the one from 'Information processing' (Response from George: Do you have a suggestion, what we could take?)
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| - |
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| - | ==Text==
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| - |
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| - | ===Motivation & Project Idea===
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| - | '''Simona''': E. lemming is the 2010 iGEM project of ETH Zurich! We are controlling the movement of any E. coli cell by hijacking chemotaxis, monitoring its spatial behavior by image processing techniques and directing it towards an user - define target by smart control algorithms! Find out more about our motivation and project idea!
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| - |
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| - | ===E. lemming - The movie===
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| - | '''Simona''': Watch a short animation of E. lemming! Find out the core concepts behind our project and how we combined biology, mathematical modeling and image processing techniques to create E. lemming!
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| - |
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| - | ===Biology & Wet Laboratory===
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| - | '''Simona''': How is it implemented? By coupling the Che proteins of the chemotaxis pathway to a synthetic light - sensitive spatial localization system, their activity can be reversibly controlled. To find out more about E. lemming on the molecular level and to find information regarding the wet laboratory experiments, visit our Biology & Wet Laboratory section.
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| - |
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| - | ===Mathematical Modeling===
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| - | '''Simona'''Mathematical Modeling
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| - | How does modeling help? To find out how the mathematical models we developed not only supported wet lab experiments by optimizing the biological network structure to be used, but also provided a test bench for our information processing system, visit the Mathematical Modeling section!
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| - |
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| - | ===Information Processing===
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| - | '''Simona''' How is it controlled? Implementation of a comprehensive information processing workflow for controlling E. lemming was achieved by combining microscopy, image analysis and processing and controlling algorithms. Find out more about how the information processing part of our project not completed E. lemming, but also created a brand new synthetic biology game: E.lemming!
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| - |
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| - | ===Achievements===
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| - | '''Simona''': OK
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| - | ==Motivation==
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| - |
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| - | = General =
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| - | * Movies: '''George & Luzi''' Almost done, but needs speech! '''Elsa'''
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| - | * Matlab Toolboxes: '''Moritz & George'''
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| - |
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| - | = Proofreading =
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| - |
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| - | ===Introduction===
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| - | * https://2010.igem.org/Team:ETHZ_Basel '''EVERYONE''': Please read every text of the teaser and suggest improvements.
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Introduction/Motivation '''EVERYONE''': Please read and suggest improvements.
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| - |
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| - | ===Biology & Wet Laboratory===
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology '''Simona DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology/Molecular_Mechanism '''George DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology/Cloning '''George DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology/Implementation '''Thanuja DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology/Archean_Light_Receptor '''Elsa'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology/Safety '''Elsa'''
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| - |
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| - | ===Mathematical Modeling===
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| - | '''Christoph will do this by Sunday'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling : first proofreading '''Simona DONE'''
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| - | Christoph:
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| - | * first box: E. lemming, these aren't the devices we used for modeling, that is what we model, anchor not necessarily the plasmid
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| - | * too many "in order to"
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| - | * mathematical modeling overview: please rearrange: 1. WHAT complex model set up, consisting of chemotaxis, light, move, implemented and coupled 2. WHY explain support a little bit more
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| - |
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| - | * Model implementation: tab and text order should be equal; implementation and adaption of literature described ones, movement by our own!
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| - |
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| - | * Combined mathematical models: shouldn't light-switch-chemo-movement be the complete?
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Combined#Light_switch_-_Chemotaxis : interfaces had to be defined, show that the individual models are without restrictons combinable by user wish, number of combinations
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Light_Switch
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| - | * "To model the relocation, we decided to adapt a model recently published by Sorokina et al [1]. As a first step we reimplemented the model as published in the paper." make one good sentence
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Chemotaxis: first proofreading '''Simona DONE'''
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| - | C: give an idea about the complexity, e.g. high number of proteins and interactions;
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| - | why did we use only Spiro and Mello?;
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| - | models: text first as it explains the plots;
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| - | please gibe a clearer description of the plots, for an external person it's almost not understandable
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Movement
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| - | * make clear we did this completely on our own, not implemented but created!; '''Great section!!!''' ''''THANKS!!!'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Combined C: see above
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Experimental_Design C: OK
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| - |
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| - | ===Information Processing===
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing '''Simona DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Microscope '''Simona DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/InformationFlow '''Simona DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/CellDetection '''Thanuja DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Visualization '''Thanuja DONE'''
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| - |
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| - | ===Achievements===
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| - |
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| - | == Pick-a-task ==
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| - | * https://2010.igem.org/Team:ETHZ_Basel: '''George DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Introduction/Motivation: '''Simona DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Introduction/Movie: '''George DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology: '''Simona DONE''' '''George DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology/Molecular_Mechanism: '''George DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology/Cloning: '''George DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology/Implementation: '''George DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology/Archean_Light_Receptor: Image: change font to Trebuchet MS, save as PNG, put Sequence into container, link references '''Elsa'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Biology/Safety: finish content '''Elsa, need help!'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling: '''Simona DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Light_Switch: '''Simona 1/2 done''' Shorten text
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Chemotaxis: '''Simona DONE''', '''George DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Movement: '''Simona DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Combined: '''Simona''' make coherent
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Modeling/Experimental_Design: '''George DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing: '''Simona DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Microscope: '''Simona DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/InformationFlow:'''Simona DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/CellDetection'''Thanuja: Done'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Visualization'''Thanuja: Done'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Controller: '''Simona''' Check spaces between paragraphs
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| - | * https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Game: Upload movie to ethzigem10 Youtube account
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Achievements: Will we have experimental date? Make otherwise overview of achievements.
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Achievements/BioBrick_Toolbox: finish content
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Achievements/Matlab_Toolbox: Arrange examples different. (remove spaces), correct references.
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Achievements/Interworking: '''Simona''' Finish content and decide upon final title.
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Achievements/Simulation: Upload movie to ethzigem10 Youtube account and finish content
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Achievements/Medal_Criteria: '''Thanuja DONE'''
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| - | * https://2010.igem.org/Team:ETHZ_Basel/Team: Moritz: 350*350px picture;
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"
